Read the system documentation!
Backup will back-up contacts, appointments, your settings and bookmark and a list of installed applications. This is held in a system directory, but can be linked to "MyDocs". This is NOT Windows. You should backup to your SD memory.
Windows does not have user protection and does not have any "x" bit to indicate that a file is "executable" - e.g. as a shell script. So, if you use FAT32 on the /rootfs - there is no way anything here can start executing, so this is used where really nothing should be executable, so just keep the executable in a directory that is linked into the FAT32 file system.
There is no way you can check, verify and repair the FAT.
Please, read the documentation, and shoud you happen to know Windows and Microsoft, please understand that this was made to fix most of the problems that Microsoft skipped, and require more than a Sunday School course to muck around with. Scrap the wizards and try to understand because here things can be explained and they make sense - curses and wizards gets you nowhere.